Hi Marja
why are you converting at all? Why not just give one of the dicom files in
the correct series to recon-all directly? I don't think we've ever seen an
orientation problem if you process that way
cheers
Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview the orientation is the same as in the
original dicoms, but the results in the .stats files made me think that left
and right might be swapped. Of course this could just really be the results
of the correct hemispheres, but that is why I asked whether you are aware of
any dimension switching during the recon-all. If not, than I can safely
assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
so you convert from dicom to nifti, then view in freeview and
you think that the anatomical orientations are incorrect? That
should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Well the DICOMs I visualized in osiriX, and the
niftis in both freesurfer
and fsl. And there they seemed to match.
So my question is; is there a possibility that
dimensions are swapped during
the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Marja
what did you visualize it in? I would suggest
freeview
cheers
Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
I converted the images with MRIconvert,
then I
swapped them in FSL with
swapdim.
I checked the images by opening the
original dicoms
and the converted
niftis, and then visually compared them
(since the
heads are not very
symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14, 2016 at 12:35 AM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Marja
how did you swap them? And more
importantly,
how did you check
that the orientations were correct
after
conversion?
cheers
Bruce
On Mon, 13 Jun 2016, Marja Caverlé
wrote:
Hi guys,
Just a quick question; I
have converted
my original
DICOMs into niftis.
After the conversion I
manually checked
whether the
orientations were still
the same, and they were not,
so I
swapped them.
After this I did a recon
-all.
A lot of my results are at
one side
while I expected
them in the other
hemisphere. Is there any
chance that the
recon -all
swapped left and right?
How to check for this? I
just want to be
sure that I
am really talking about
the right hemisphere.
Thanks!
Best,
Marja
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
intended only for
the person to whom
it is
addressed. If you believe this e-mail
was sent to
you in error and the
e-mail
contains patient information, please
contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline .
If the
e-mail was sent to you
in error
but does not contain patient
information, please
contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for
the person to whom
it is
addressed. If you believe this e-mail was sent to
you in error and the
e-mail
contains patient information, please contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the
e-mail was sent to you
in error
but does not contain patient information, please
contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
